Later that year, while traveling back to the Enterprise by runabout, the starboard antimatter pod has been completely drained, despite the fact that there was no leak and all of the other engine systems were fully operational. It turned out that the runabout had entered a region of temporal fragments that made the antimatter pod work longer than the rest of the shuttle had. (TNG: "Timescape")

We can assume that antimatter pods are self-contained and survive some sorts of disasters aboard starships, such as the destruction of the starship, uncontrolled entry into an atmosphere, etc. This is because vehicles in the Star Trek universe do not consistently explode on every single occasion a vessel is catastrophically damaged. It is probably safe to assume that each pod has its own battery, or other power source to maintain the containment field, or some kind of post-exhaustion flush method. This way, it is believable that a free floating antimatter pod from a destroyed starship, or a pod remaining in a derelict hulk, could remain intact until such a time as all of the antimatter within was expended.